South Australian babies and young people will be the first in the nation to receive free meningococcal B vaccinations through a new program.

The State Government announced it would be rolled out from October, with vaccinations to be provided by GPs, local government immunisation clinics, Aboriginal Health Services, Child and Family Health Services and Country Health SA.

The targeted vaccination program would initially be for babies aged between six weeks and one year, and children under the age of four.

From 2019 the program would be expanded to include catch up programs for students in years 10 and 11, as well as young people aged from 17 to 20 years.

South Australia has the worst meningococcal B rates in the country, and an expert working group estimated the scheme would prevent on average 12 cases of the disease each year, and save one life every two years.

The life-threatening disease can also cause life-long disabilities.

However despite announcing the imminent rollout of the vaccine, Health Minister Stephen Wade was unable to say how much it would cost taxpayers, as the Government was still negotiating with the vaccine supplier.

He insisted enough had been budgeted to cover the maximum possible cost.

"What we don't know at this stage is what the lower cost might be," Mr Wade said.

"If we make savings we'll welcome those.

"I do not want to do anything that prejudices the commercial negotiations, because I want to get the best possible outcome for South Australians."

Costings released by the Labor Party in the lead up to the March state election predicted the vaccine would cost approximately $90 per dose, with young children requiring four doses, equivalent to $7.2 million a year to cover the 20,000 babies born on average per year.

SA Health's chief public health officer Paddy Phillips said the groups eligible for the free vaccine would provide the best coverage for the disease.

"We know that meningococcal B disease occurs more frequently in infants and children up to four years of age, and young adults aged between 15 and 20 years of age," Professor Phillips said.

"There have been 372 cases of meningococcal B disease in SA since 2000, which sadly includes 14 deaths, and of those cases more than 60 per cent were in people aged under 21."

He said he was confident the program would have ample supply of vaccination supplies.

'It's worth every cent'

Amy Wales' son Riley Nixon, now 4, contracted meningococcal B just before his second birthday.

After four days in hospital, he had to have both legs amputated above the knee, as well as virtually all of his fingers.

"We still have him, we're technically one of the lucky ones, even though it's pretty brutal what he's been through," Ms Wales said.

"He's the strength of the whole family… straight after the amputations we ended up taping pencils to his hands because he just wanted to draw."

"He's got prosthetic legs but he's quicker on his bum, doesn't care what he looks like."

At the time Ms Wales had assumed Riley was already vaccinated for Meningococcal B through the national immunisation program.

"We've been constantly advocating for awareness, for vaccinations," she said.

"If it helps even one person not go through what we've been through, it's worth every cent."